tbuckley/cabot-search huggingface dataset:
Glioblastoma Spheroid Invasion through Soft, Brain‐Like Matrices Depends on Hyaluronic Acid–CD44 Interactions (Adv. Healthcare Mater. 14/2023)
Authors: Gevick Safarians, Alireza Sohrabi, Itay Solomon, Weikun Xiao, Soniya Bastola, Bushra W. Rajput, Mary Epperson, Isabella Rosenzweig, Kelly Tamura, Breahna Singer, Joyce Huang, Mollie J. Harrison, Talia Sanazzaro, Michael C. Condro, Harley I. Kornblum, Stephanie K. Seidlits
Journal: Advanced Healthcare Materials (2023)

Glioblastoma Tumors Glioblastoma (GBM) tumors aggressively invade the brain and are highly lethal. Hyaluronic acid (HA), a polysaccharide ubiquitous in the brain extracellular matrix, is overexpressed in GBM tumors. Using patient-derived GBM cells and engineered, 3D culture microenvironments, article 2203143 by Stephanie K. Seidlits and co-workers demonstrates a biphasic relationship between invasive activity and HA concentration that depends on phosphorylation of ezrin downstream of the CD44 receptor.
Abstract IA007: Science of prostate cancer care and survivorship in black men: Structural, social and biological determinants
Authors: Folakemi Odedina, Roxana Dronca, Kimlin Ashing, Ernest Kaninjing, Solomon Rotimi, Che Ngufor
Journal: Cancer Research (2023)

Abstract Black men are disproportionately affected by prostate cancer (CaP), with limited progress in closing the CaP care and survivorship gaps experienced by Black men compared to other racial/ethnic groups. Unfortunately, there is an uptick in CaP incidence rate in the United States (US) since 2014. As reported by the American Cancer Society, the rising CaP incidence rate indicates a shift towards higher grade and stage during diagnosis. The prostate cancer (CaP) disparities experienced by Black men in the US is a microcosm of the global burden of CaP seen in men of African ancestry. For example, the top ten countries leading CaP mortality in the world are all Black nations in Africa and the Caribbean. The complexity of CaP disparities and the need for a unique approach to better understand and address a complex chronic disease, such as CaP, underscores the need for consortium research that is multilevel, collaborative, translational, and global. Through the Department of Defense funding, we formed an inclusive Cancer Care Research Equity (iCCaRE) for Black Men Consortium to advance health equity and reduce disparities in CaP. Comprising CaP survivors, advocates, scientists, and clinicians, the iCCaRE for Black Men Consortium addresses structural, social and biological determinants of CaP among ethnically diverse Black men globally, including US Black men, West African immigrant men in the US and indigenous West African men. The overall goal of the iCCaRE consortium is to optimize CaP diagnosis experiences, treatment and survivorship based on the Science of Survivorship (SOS). Our central hypothesis is that improving social-determinants of health (SDOH) factors, CaP care and survivorship (CaPCaS)-related factors and mediating biological factors will lead to an improvement in patient-reported outcomes (PROs). This presentation will highlight the structural inequities, societal injustices and biological determinants found to be associated with CaP care and survivorship among Black men. Additionally, we will present the use of Community Living Lab (CoLLab) Health System approach to address inequity in minoritized and marginalized communities. Citation Format: Folakemi Odedina, Roxana Dronca, Kimlin Ashing, Ernest Kaninjing, Solomon Rotimi, Che Ngufor, Arnold Merriweather, iCCaRE Consortium. Science of prostate cancer care and survivorship in black men: Structural, social and biological determinants [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr IA007.
Abstract B006: Identifying the molecular signature of bi-potent prostate epithelial cells through scRNA-seq
Authors: Hunain Khawaja, Cynthia Miranti
Journal: Cancer Research (2023)

Abstract Introduction: Recent studies have shown that cells undergoing oncogenic processes usurp normal developmental pathways to escape regulators of unsolicited growth. Basal to luminal differentiation in the prostate serves as another cellular process that can go awry, the dysregulation of which can enable oncogenesis in the prostate. Studies have found bi-potent cells in prostate epithelium and speculate those to be cells of origin in prostate cancer. Methods and Results: Through single-cell RNA sequencing we investigated basal to luminal differentiation of normal human prostate epithelial cells across timepoints Days 0, 4, 8, 12, 16, and 20 by stimulating with FGF-7 (20ng/mL) and R1881 (10nM) and explored the data to identify unique populations present in the differentiation process. Our results show spatial separation at various timepoints with distinct transcriptomics profile at Day 0, Day 16, and Day 20. As expected, populations present at Day 0 are also present across all timepoint, though enrichment of various distinct populations emerged throughout the differentiation process. Using trajectory analysis (Monocle3) and the Cell Surface Protein Atlas, we profiled surface proteins for each cluster at Day 0 and identified a set of unique surface markers (SLC3A, LYPD3, TACSTD2, DSC2) from undifferentiated basal cells that express both basal (TP63+, K14+) and luminal markers (K8+, K18+), potentially serving as a bi-potent prostate epithelial cells. Conclusion: Our data have identified unique populations present in our prostate differentiation model expressing both luminal and basal signatures which can be isolated using identified surface markers to investigate the role of bi-potent cells in prostate differentiation and oncogenesis. Citation Format: Hunain Khawaja, Cynthia Miranti. Identifying the molecular signature of bi-potent prostate epithelial cells through scRNA-seq [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B006.
Abstract PR001: An endogenous molecular brake preventing APOBEC-driven tumor mutational burden, heterogeneity and AR therapy resistance
Authors: Ping Mu, Xiaoling Li, Yunguan Wang
Journal: Cancer Research (2023)

Abstract Tumor mutational burden and heterogeneity fuel resistance to many targeted therapies, which inevitably limits the clinical outcome of patients. The cytosine deaminase APOBEC proteins are major drivers of mutagenesis in human cancer, with over 70% of tumors exhibiting a mutational signature that is impacted by APOBEC activity. Nevertheless, the mechanisms through which tumor cells hijack the powerful APOBEC mutagenesis machinery to promote heterogeneity and therapy resistance remain largely unknown. Through a multi-disciplinary approach integrating bulk and single cell RNA-Seq (scRNA-Seq), whole-genome exome-sequencing (WES), and CRISPR library screening, we identified a long sought-after cell-intrinsic mechanism that prevents APOBEC-driven mutagenesis in non-malignant cells. The loss of this “molecular brake” unleashes APOBEC3B-driven mutagenesis in malignant cells, which then becomes a key mutator and represents the long sought-after molecular source of driver mutations in some frequently mutated genes in cancers, including FOXA1, EP300, and AR. Functional screening identified eight crucial drivers for Androgen Receptor (AR)-targeted therapy resistance in prostate cancer that are mutated by APOBEC3B: BRD7, CBX8, EP300, FOXA1, HDAC5, HSF4, STAT3, and AR. Finally, contrary to conventional understanding, our study reveals that driver mutations in FOXA1 induced by APOBEC3B, not mutations in AR, evolutionarily outcompete other driver mutations and eventually dominate the resistant tumors. Collectively, these results uncover a cell-intrinsic mechanism that unleashes APOBEC-driven mutagenesis, which plays a significant role in conferring targeted therapy resistance and could be the potential therapeutic targets to overcome resistance. Citation Format: Ping Mu, Xiaoling Li, Yunguan Wang. An endogenous molecular brake preventing APOBEC-driven tumor mutational burden, heterogeneity and AR therapy resistance [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr PR001.
Abstract B005: The oncogenic transcription factor ERG has distinct roles and signaling regulation in different prostate cancer cell types
Authors: Peter C. Hollenhorst, Saranya Rajendran, Travis J. Jerde
Journal: Cancer Research (2023)

Abstract Background: ERG is the most common oncogene in prostate cancer, as it is aberrantly expressed in about 50% of cases due to the TMPRSS2/ERG gene rearrangement. ERG is not normally expressed in the adult prostate. The normal function of ERG is confined to hematopoietic stem cells and blood vessels. Aberrant expression of ERG in prostate epithelial cells is oncogenic when combined with mutations that activate the PI3K/AKT signaling pathway. The RAS/MAPK pathway can also regulate ERG function through direct phosphorylation of ERG by ERK. The function of these regulatory events and how they can be exploited to develop therapy for ERG-positive prostate cancer remains unclear. Results: ERG expression in prostate basal epithelial cells drives epithelial to mesenchymal transition and stemness properties. This function requires ERG phosphorylation via a positive feedback loop with the TLR4 signaling pathway, and can be repressed by a TLR4 inhibitor. Activation of the PI3K/AKT pathway rearranges the ERG cistrome and alters ERG function, where ERG now promotes luminal epithelial differentiation. In the presence of activated AKT, new ERG targets include genes involved in vascular development and ERG phosphorylation is regulated through a positive feedback loop with the VEGF signaling pathway. Conclusions: ERG function in basal and luminal prostate epithelial cells appear to mirror ERG functions in hematopoietic stem cells and blood vessels, respectively. These findings suggest strategies of combinatorial inhibition of ERG function in both cell types. Citation Format: Peter C. Hollenhorst, Saranya Rajendran, Travis J. Jerde. The oncogenic transcription factor ERG has distinct roles and signaling regulation in different prostate cancer cell types [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B005.
Abstract A077: MicroRNA drivers of resistance to androgen deprivation therapy in prostate cancer
Authors: Philippa C. Saunders, Claire Fletcher
Journal: Cancer Research (2023)

Abstract INTRODUCTION: Prostate cancer is the most prevalent malignancy affecting Western males. It is initially an androgen-dependent disease: androgens bind to the androgen receptor and drive expression of genes that promote proliferation and evasion of apoptosis. Despite reduced androgen dependence in advanced prostate cancer, androgen receptor signalling remains a key driver of growth. Androgen deprivation therapy (ADT) is therefore a first line treatment approach and works well initially, but resistance inevitably develops. Abiraterone and Enzalutamide are drugs widely used in ADT and are androgen synthesis and androgen receptor signalling inhibitors respectively. The shortage of other treatment options means acquired resistance to these drugs is a major clinical problem. MicroRNAs (miRs) are important mediators of post-transcriptional gene regulation and show altered expression in cancer. Several have been linked to the development of resistance to ADT. Manipulation of such miRs may be a pathway to breakthrough treatments for advanced prostate cancer. This study aimed to validate ADT resistance-implicated miRs and their clinically relevant targets. MATERIALS AND METHODS: Small RNA-sequencing of Abiraterone- and Enzalutamide-resistant C42 prostate cancer cells identified subsets of miRs dysregulated as compared to parental cells. Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) was used to validate altered expression of candidate ADT resistance-implicated miRs 195-5p, 497-5p and 29a-5p in ADT-resistant and -responsive prostate cancer cell lines, patient-derived xenografts (PDXs) and primary prostate cancer explants. RESULTS AND DISCUSSION: This study suggests a possible role for miR-497-5p in the development of ADT resistance in prostate cancer. MiR-497-5p expression was increased in ADT-resistant versus ADT-responsive prostate cancer cells. Importantly, miR-497-5p expression was also increased in Enzalutamide-treated, castrated (ADT-mimicking) PDXs versus intact PDXs. MiR-195-5p was also elevated in ADT-resistant versus -responsive prostate cancer cells, while there was a drop in miR-29a-5p expression. Candidate clinically relevant targets of miR-497-5p in prostate cancer were identified by mining AGO-PAR-CLIP-seq data sets and may include AVL9 and FZD6. CONCLUSION: In summary, this study identified microRNAs that are implicated in prostate cancer resistance to androgen deprivation therapy and could represent novel therapeutic targets for advanced disease. Citation Format: Philippa C. Saunders, Claire Fletcher. MicroRNA drivers of resistance to androgen deprivation therapy in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A077.
Abstract A027: Identification and characterization of PLUTO-201, a novel lncRNA associated with prostate cancer metastasis
Authors: Haolong Li, Noah Younger, Hyun Jin Shin, Bhavna Malik, Shuang G. Zhao, Sethuramasundaram Pitchiaya, Marsha Calvert, Meng Zhang, Laura Chang, Lisa Chesner, Junjie Hua, Kathy Li, Vishal Kothari, Emily Egusa, Jonathan Chou, Rajdeep Das, Alma Burlingame, Arul M. Chinnaiyan, Hui Li, Felix Y. Feng
Journal: Cancer Research (2023)

Abstract Prostate cancer is the most common non-cutaneous malignancy in men, accounting for approximately 268,000 cases and 35,000 deaths in the United States each year. This disease is a heterogeneous entity with a wide spectrum of clinical behaviors and outcomes - while a majority of men will be cured of early-stage prostate cancer, approximately 20% will develop metastatic disease, which is incurable and ultimately fatal. Despite extensive investigation, the factors promoting aggressive prostate cancer are incompletely understood. Using recently reported microarray data representing a comprehensive analysis of lncRNA prevalence across thousands of patients with prostate cancer, we now report the identification of a novel lncRNA, Prostate Locus of Uncharacterized Transcript Outlier 201 (PLUTO-201), which is strongly associated with metastasis and poor overall survival in men with prostate cancer. We find that in vitro manipulation of PLUTO-201 expression levels in prostate cancer cell lines modulates proliferation rates and markers of aggressive phenotype. Further investigation shows that PLUTO-201 localizes to the nucleus and regulates transcription of multiple genes including those responsible for steroid biosynthesis and the MHC class 1 complex, driving increased growth in androgen-depleted conditions and decreased susceptibility to T cell-mediated cytotoxicity. Overall, our findings nominate PLUTO-201 as a driver of aggressive prostate cancer phenotypes and poor clinical outcomes and suggest possible mechanisms accounting for this activity. Citation Format: Haolong Li, Noah Younger, Hyun Jin Shin, Bhavna Malik, Shuang G. Zhao, Sethuramasundaram Pitchiaya, Marsha Calvert, Meng Zhang, Laura Chang, Lisa Chesner, Junjie Hua, Kathy Li, Vishal Kothari, Emily Egusa, Jonathan Chou, Rajdeep Das, Alma Burlingame, Arul M. Chinnaiyan, Hui Li, Felix Y. Feng. Identification and characterization of PLUTO-201, a novel lncRNA associated with prostate cancer metastasis [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A027.
Abstract A022: Alternative polyadenylation as a therapeutic vulnerability in prostate cancer
Authors: Kiel T. Tietz, Braedan M. McClukey, Sarah A. Munro, Conor R. Miller, Scott M. Dehm
Journal: Cancer Research (2023)

Abstract Prostate cancer is the second leading cause of male cancer death in the United States. While localized disease can be cured by radiation or surgery, metastatic prostate cancer presents a clinical challenge. Metastatic prostate cancer can initially be controlled by endocrine therapies that target the androgen receptor (AR), however, these tumors will inevitably develop resistance. This stage of the disease, termed castration-resistant prostate cancer (CRPC), is responsible for the majority of prostate cancer-specific deaths. Current treatment options for CRPC patients are not curable and highlight the need to develop novel therapeutic options that will more effectively treat the disease. Spliced mRNA molecules undergo cleavage and polyadenylation ~25 base pair downstream from a canonical 5’AAUAAA poly(A) site located within the 3’ untranslated region (UTR). Shortening of mRNA 3’UTRs through alternative polyadenylation has been found in numerous cancers leading to downregulation of tumor suppressor genes and upregulation of oncogenes. To investigate the function of alternative polyadenylation in CRPC, we conducted a loss-of-function screen of mRNA polyadenylation factors in hormone-sensitive LNCaP cells and hormone-insensitive LNCaP95 and 22Rv1 cells. We found that knockdown of the cleavage and polyadenylation specificity factor (CPSF) component, CPSF1, inhibited growth of all cell lines. To define pathways that are regulated by CPSF1 in prostate cancer, we identified CPSF1-dependent gene expression using RNA-seq and CPSF1-dependent poly(A) sites using poly(A)-ClickSeq (PAC-Seq). Gene set enrichment analysis of RNA-seq data revealed the Glycolysis Hallmark and Hypoxia Hallmark gene sets were positively regulated by CPSF1. Analysis of PAC-seq data revealed global induction of poly(A) sites distal to 3’ UTRs upon CPSF1 knockdown. By integrating these RNA-seq and PAC-seq datasets, we have identified AR-independent pathways that may be attractive for therapeutic targeting in prostate cancer. This study has revealed post-transcriptional gene regulation by CPSF1 as an important pathway used in CRPC. Citation Format: Kiel T. Tietz, Braedan M. McClukey, Sarah A. Munro, Conor R. Miller, Scott M. Dehm. Alternative polyadenylation as a therapeutic vulnerability in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr A022.
Abstract PR008: Molecular determinants of prostate cancer lineage plasticity
Authors: Kristine Wadosky, Sheng-Yu Ku, Yanqing Wang, Xiaojing Zhang, Jie Wang, Jianmin Wang, Himisha Beltran, David W. Goodrich
Journal: Cancer Research (2023)

Abstract Androgen deprivation therapy (ADT) has been an effective treatment for advanced prostate cancer (PCa) for decades because PCa retains the lineage specific dependence of normal prostate tissue on androgen receptor (AR) signaling. Unfortunately, nearly all patients will progress through ADT with castrate resistant prostate cancer (CRPC). CRPC is typically associated with reactivation of AR signaling despite ADT. However with widespread clinical deployment of potent AR signaling inhibitors, an increasing fraction of CRPCs (~20) are now observed to lose AR signaling activity and show gene expression patterns consistent with alternative lineage states. These lineage variants share clonal origin with the pre-existing adenocarcinoma, so some PCa cells have sufficient plasticity to reprogram to an AR independent lineage state like neuroendocrine prostate cancer (NEPC) that is recalcitrant to available therapies. The molecular determinants of prostate cancer lineage plasticity are incompletely defined, and this knowledge gap has hindered development of diagnostic and therapeutic approaches necessary to identify and treat prostate cancer lineage plasticity. We present results from experiments testing the contribution of EZH2 and NOTCH signaling to prostate cancer lineage plasticity and NEPC reprogramming. EZH2 expression is elevated in advanced PCa, particularly NEPC, suggesting it drives lineage reprogramming. However, using genetically engineered mice and organoids we find that EZH2 is not required for NEPC reprogramming that occurs in some PCa cells in the absence of the RB1 and TP53 tumor suppressor genes. EZH2 deficiency does alter multi-lineage prostate cancer plasticity, biasing development towards lineage variants observed clinically including amphicrine and double negative prostate cancer. In contrast, data from clinical specimens indicates NOTCH signaling activity declines in NEPC compared to AR+ CRPC. NOTCH signaling suppresses NEPC development in both organoids and genetically engineered mice, and loss of NOTCH signaling is required to maintain the NEPC lineage state. Constitutive NOTCH signaling biases PCa development towards unique lineage variants including AR positive metastatic PCa with luminal differentiation. These results identify EZH2 and NOTCH signaling as molecular determinants of PCa lineage plasticity and NEPC reprogramming with implications for ongoing efforts to target these molecules for PCa therapy. Citation Format: Kristine Wadosky, Sheng-Yu Ku, Yanqing Wang, Xiaojing Zhang, Jie Wang, Jianmin Wang, Himisha Beltran, David W. Goodrich. Molecular determinants of prostate cancer lineage plasticity [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr PR008.